Purpose: Full-mouth disinfection enables to reduce the probability of cross contamination from untreated pockets to treated ones, for completing the entire SRP under local anesthesia with chlorhexidine as a mouth wash in two visits within 24 hours. This study aimed to compare the clinical effects of modified full-mouth disinfection (Fdis) after 6 months with those of conventional SRP (cSRP). Methods: Thirty non-smoking chronic periodontitis subjects were randomly allocated two groups. The Fdis group underwent the entire SRP under local anesthesia in two visits within 24 hours, a week after receiving supragingival scaling. A chlorhexidine (0.1%) solution was used for rinsing and subgingival irrigation for Fdis. The cSRP group received SRP per quadrant under local anesthesia at one-week intervals, one week after they had received scaling. Clinical parameters were recorded at baseline, after 1, 3 and 6 months. Results: There are significant (P<0.05) decreases in the sulcus bleeding ind